Biological Assembly 1  

 3D View: Structure

Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.27 kDa 
• Atom Count: 3517 
• Residue Count: 439 
• Unique protein chains: 3

1KC5

CRYSTAL STRUCTURE OF ANTIBODY PC287 IN COMPLEX WITH PS1 PEPTIDE

• DOI: 10.2210/pdb1KC5/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2001-11-07 Released: 2002-07-24 
• Deposition Author(s): Nair, D.T., Singh, K., Siddiqui, Z., Nayak, B.P., Rao, K.V., Salunke, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.270 
• R-Value Work: 0.195 

Literature

Epitope recognition by diverse antibodies suggests conformational convergence in an antibody response.

Nair, D.T., Singh, K., Siddiqui, Z., Nayak, B.P., Rao, K.V., Salunke, D.M.

(2002) J Immunol 168: 2371-2382

• PubMed: 11859128 
• DOI: 10.4049/jimmunol.168.5.2371
• Primary Citation of Related Structures:  
  1KC5, 1KCV, 1KCU, 1KCS


• PubMed Abstract: 
  

Crystal structures of distinct mAbs that recognize a common epitope of a peptide Ag have been determined and analyzed in the unbound and bound forms. These Abs display dissimilar binding site structures in the absence of the Ag. The dissimilarity is primarily expressed in the conformations of complementarity-determining region H3, which is responsible for defining the epitope specificity. Interestingly, however, the three Abs exhibit similar complementarity-determining region conformations in the Ag binding site while recognizing the common epitope, indicating that different pathways of binding are used for Ag recognition. The epitope also exhibits conformational similarity when bound to each of these Abs, although the peptide Ag was otherwise flexible. The observed conformational convergence in the epitope and the Ag binding site was facilitated by the plasticity in the nature of interactions.

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Related Citations: 

• Crystal Structure of an Antibody Bound to an Immunodominant Peptide Epitope: Novel Features in Peptide-antibody Recognition
  Nair, D.T., Singh, K., Sahu, N., Rao, K.V., Salunke, D.M.
  (2000) J Immunol 165: 6949

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Organizational Affiliation: 

Structural Biology Unit, National Institute of Immunology, New Delhi 110067, India.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PC287 Immunoglobulin	L	214	Mus musculus	Mutation(s): 0  Gene Names: Igkc
Find proteins for P01837 (Mus musculus) Explore P01837  Go to UniProtKB:  P01837

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PC287 Immunoglobulin	H	217	Mus musculus	Mutation(s): 0  Gene Names: Ighg1, Igh-4
Find proteins for P01869 (Mus musculus) Explore P01869  Go to UniProtKB:  P01869

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PS1 peptide	P	15	N/A	Mutation(s): 0
Find proteins for Q91C35 (Hepatitis B virus genotype A1 subtype adw2 (isolate South Africa/84/2001)) Explore Q91C35  Go to UniProtKB:  Q91C35

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.270 
• R-Value Work: 0.195 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.59	α = 90
b = 71.588	β = 98.09
c = 87.677	γ = 90

Software Package:

Software Name	Purpose
MAR	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
MAR	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-11-07 
• Released Date: 2002-07-24 
Deposition Author(s): Nair, D.T., Singh, K., Siddiqui, Z., Nayak, B.P., Rao, K.V., Salunke, D.M.

Revision History 

• Version 1.0: 2002-07-24
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance